Database Engines for Geographical Information Systems

Our ability to identify, acquire, store, enquire on and analyse data is increasing as never before, especially in the GIS field. Technologies are becoming available to manage a wider variety of data and to make intelligent inferences on that data. The mainstream arrival of large-scale database engines is not far away. The experience of using the first such products tells us that they will radically change data management in the GIS field.

Endemic tuberculosis, the homeless, and public transportation: A merging of geographical information systems surveillance and the Houston Tuberculosis Initiative Surveillance project

To reach the goals established by the Institute of Medicine (IOM) and the Centers for Disease Control's (CDC) STOP TB USA, measures must be taken to curtail a future peak in Tuberculosis (TB) incidence and speed the currently stagnant rate of TB elimination. Both efforts will require, at minimum, the consideration and understanding of the third dimension of TB transmission: the location-based spread of an airborne pathogen among persons known and unknown to each other. This consideration will require an elucidation of the areas within the U.S. that have endemic TB. The Houston Tuberculosis Initiative (HTI) was a population-based active surveillance of confirmed Houston/Harris County TB cases from 1995–2004. Strengths in this dataset include the molecular characterization of laboratory confirmed cases, the collection of geographic locations (including home addresses) frequented by cases, and the HTI time period that parallels a decline in TB incidence in the United States (U.S.). The HTI dataset was used in this secondary data analysis to implement a GIS analysis of TB cases, the locations frequented by cases, and their association with risk factors associated with TB transmission. ^ This study reports, for the first time, the incidence of TB among the homeless in Houston, Texas. The homeless are an at-risk population for TB disease, yet they are also a population whose TB incidence has been unknown and unreported due to their non-enumeration. The first section of this dissertation identifies local areas in Houston with endemic TB disease. Many Houston TB cases who reported living in these endemic areas also share the TB risk factor of current or recent homelessness. Merging the 2004–2005 Houston enumeration of the homeless with historical HTI surveillance data of TB cases in Houston enabled this first-time report of TB risk among the homeless in Houston. The homeless were more likely to be US-born, belong to a genotypic cluster, and belong to a cluster of a larger size. The calculated average incidence among homeless persons was 411/100,000, compared to 9.5/100,000 among housed. These alarming rates are not driven by a co-infection but by social determinants. The unsheltered persons were hospitalized more days and required more follow-up time by staff than those who reported a steady housing situation. The homeless are a specific example of the increased targeting of prevention dollars that could occur if TB rates were reported for specific areas with known health disparities rather than as a generalized rate normalized over a diverse population. ^ It has been estimated that 27% of Houstonians use public transportation. The city layout allows bus routes to run like veins connecting even the most diverse of populations within the metropolitan area. Secondary data analysis of frequent bus use (defined as riding a route weekly) among TB cases was assessed for its relationship with known TB risk factors. The spatial distribution of genotypic clusters associated with bus use was assessed, along with the reported routes and epidemiologic-links among cases belonging to the identified clusters. ^ TB cases who reported frequent bus use were more likely to have demographic and social risk factors associated with poverty, immune suppression and health disparities. An equal proportion of bus riders and non-bus riders were cultured for Mycobacterium tuberculosis, yet 75% of bus riders were genotypically clustered, indicating recent transmission, compared to 56% of non-bus riders (OR=2.4, 95%CI(2.0, 2.8), p<0.001). Bus riders had a mean cluster size of 50.14 vs. 28.9 (p<0.001). Second order spatial analysis of clustered fingerprint 2 (n=122), a Beijing family cluster, revealed geographic clustering among cases based on their report of bus use. Univariate and multivariate analysis of routes reported by cases belonging to these clusters found that 10 of the 14 clusters were associated with use. Individual Metro routes, including one route servicing the local hospitals, were found to be risk factors for belonging to a cluster shown to be endemic in Houston. The routes themselves geographically connect the census tracts previously identified as having endemic TB. 78% (15/23) of Houston Metro routes investigated had one or more print groups reporting frequent use for every HTI study year. We present data on three specific but clonally related print groups and show that bus-use is clustered in time by route and is the only known link between cases in one of the three prints: print 22. (Abstract shortened by UMI.)^

Incorporating level set methods in Geographical Information Systems (GIS) for land-surface process modelling

Land-surface processes include a broad class of models that operate at a landscape scale. Current modelling approaches tend to be specialised towards one type of process, yet it is the interaction of processes that is increasing seen as important to obtain a more integrated approach to land management. This paper presents a technique and a tool that may be applied generically to landscape processes. The technique tracks moving interfaces across landscapes for processes such as water flow, biochemical diffusion, and plant dispersal. Its theoretical development applies a Lagrangian approach to motion over a Eulerian grid space by tracking quantities across a landscape as an evolving front. An algorithm for this technique, called level set method, is implemented in a geographical information system (GIS). It fits with a field data model in GIS and is implemented as operators in map algebra. The paper describes an implementation of the level set methods in a map algebra programming language, called MapScript, and gives example program scripts for applications in ecology and hydrology.

Molecular docking and geographical information systems as tools to assess the potential impact of veterinary medicines on non-target organisms and the environment

Veterinary medicines (VMs) from agricultural industry can enter the environment in a number of ways. This includes direct exposure through aquaculture, accidental spillage and disposal, and indirect entry by leaching from manure or runoff after treatment. Many compounds used in animal treatments have ecotoxic properties that may have chronic or sometimes lethal effects when they come into contact with non-target organisms. VMs enter the environment in mixtures, potentially having additive effects. Traditional ecotoxicology tests are used to determine the lethal and sometimes reproductive effects on freshwater and terrestrial organisms. However, organisms used in ecotoxicology tests can be unrepresentative of the populations that are likely to be exposed to the compound in the environment. Most often the tests are on single compound toxicity but mixture effects may be significant and should be included in ecotoxicology testing. This work investigates the use, measured environmental concentrations (MECs) and potential impact of sea lice treatments on salmon farms in Scotland. Alternative methods for ecotoxicology testing including mixture toxicity, and the use of in silico techniques to predict the chronic impact of VMs on different species of aquatic organisms were also investigated. The Scottish Environmental Protection Agency (SEPA) provided information on the use of five sea lice treatments from 2008-2011 on Scottish salmon farms. This information was combined with the recently available data on sediment MECs for the years 2009-2012 provided by SEPA using ArcGIS 10.1. In depth analysis of this data showed that from a total of 55 sites, 30 sites had a MEC higher than the maximum allowable concentration (MAC) as set out by SEPA for emamectin benzoate and 7 sites had a higher MEC than MAC for teflubenzuron. A number of sites that were up to 16 km away from the nearest salmon farm reported as using either emamectin benzoate or teflubenzuron measured positive for the two treatments. There was no relationship between current direction and the distribution of the sea lice treatments, nor was there any evidence for alternative sources of the compounds e.g. land treatments. The sites that had MECs higher than the MAC could pose a risk to non-target organisms and disrupt the species dynamics of the area. There was evidence that some marine protected sites might be at risk of exposure to these compounds. To complement this work, effects on acute mixture toxicity of the 5 sea lice treatments, plus one major metabolite 3-phenoxybenzoic acid (3PBA), were measured using an assay using the bioluminescent bacteria Aliivibrio fischeri. When exposed to the 5 sea lice treatments and 3PBA A. fischeri showed a response to 3PBA, emamectin benzoate and azamethiphos as well as combinations of the three. In order to establish any additive effect of the sea lice treatments, the efficacy of two mixture prediction equations, concentration addition (CA) and independent action ii(IA) were tested using the results from single compound dose response curves. In this instance IA was the more effective prediction method with a linear regression confidence interval of 82.6% compared with 22.6% of CA. In silico molecular docking was carried out to predict the chronic effects of 15 VMs (including the five used as sea lice control). Molecular docking has been proposed as an alternative screening method for the chronic effects of large animal treatments on non-target organisms. Oestrogen receptor alpha (ERα) of 7 non-target bony fish and the African clawed frog Xenopus laevis were modelled using SwissModel. These models were then ‘docked’ to oestradiol, the synthetic oestrogen ethinylestradiol, two known xenoestrogens dichlorodiphenyltrichloroethane (DDT) and bisphenol A (BPA), the antioestrogen breast cancer treatment tamoxifen and 15 VMs using Auto Dock 4. Based on the results of this work, four VMs were identified as being possible xenoestrogens or anti-oestrogens; these were cypermethrin, deltamethrin, fenbendazole and teflubenzuron. Further investigation, using in vitro assays, into these four VMs has been suggested as future work. A modified recombinant yeast oestrogen screen (YES) was attempted using the cDNA of the ERα of the zebrafish Danio rerio and the rainbow trout Oncorhynchus mykiss. Due to time and difficulties in cloning protocols this work was unable to be completed. Use of such in vitro assays would allow for further investigation of the highlighted VMs into their oestrogenic potential. In conclusion, VMs used as sea lice treatments, such as teflubenzuron and emamectin benzoate may be more persistent and have a wider range in the environment than previously thought. Mixtures of sea lice treatments have been found to persist together in the environment, and effects of these mixtures on the bacteria A. fischeri can be predicted using the IA equation. Finally, molecular docking may be a suitable tool to predict chronic endocrine disrupting effects and identify varying degrees of impact on the ERα of nine species of aquatic organisms.

How can geographical information systems and spatial analysis inform a response to prescription opioid misuse? a discussion in the context of existing literature

Forest cover monitoring in the Bara district (Nepal) with remote sensing and geographic information systems

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

The implementation of an Enterprise Geographical Information System to support Cadastre and Expropriation activities.

The processes of mobilization of land for infrastructures of public and private domain are developed according to proper legal frameworks and systematically confronted with the impoverished national situation as regards the cadastral identification and regularization, which leads to big inefficiencies, sometimes with very negative impact to the overall effectiveness. This project report describes Ferbritas Cadastre Information System (FBSIC) project and tools, which in conjunction with other applications, allow managing the entire life-cycle of Land Acquisition and Cadastre, including support to field activities with the integration of information collected in the field, the development of multi-criteria analysis information, monitoring all information in the exploration stage, and the automated generation of outputs. The benefits are evident at the level of operational efficiency, including tools that enable process integration and standardization of procedures, facilitate analysis and quality control and maximize performance in the acquisition, maintenance and management of registration information and expropriation (expropriation projects). Therefore, the implemented system achieves levels of robustness, comprehensiveness, openness, scalability and reliability suitable for a structural platform. The resultant solution, FBSIC, is a fit-for-purpose cadastre information system rooted in the field of railway infrastructures. FBSIC integrating nature of allows: to accomplish present needs and scale to meet future services; to collect, maintain, manage and share all information in one common platform, and transform it into knowledge; to relate with other platforms; to increase accuracy and productivity of business processes related with land property management.

Unlocking Geographical Information from Academia: an Open Source WebGIS Solution

Los Centros de Investigación de Geografía son por lo general productores de un gran volumen de Información Geográfica (IG), los cuales generan tanto proyectos financiados como iniciativas de investigación individuales. El Centro de Estudos de Geografia e Planeamento Regional (e-GEO) ha estado involucrado en varios proyectos a escala local, regional, nacional e internacional. Recientemente, dos cuestiones fueron objeto de debate. Una de ellas fue el hecho de que la información espacial obtenida a partir del desarrollo de tales proyectos de investigación no ha tenido la visibilidad que se esperaba. En la mayoría de las veces, la IG de estos proyectos no estaba en el formato adecuado para que los investigadores -o incluso el público en general o grupos de interés- pudieran pesquisar fácilmente. La segunda cuestión era sobre cómo hacer que estos resultados pudieran ser accesibles al alcance de todos, en todos los lugares, fácilmente y con los mínimos costes para el Centro, teniendo en cuenta el actual contexto económico portugués y los intereses de e-GEO. Estas dos cuestiones se resuelven con una sola respuesta: la puesta en marcha de un WebGIS en una plataforma Open Source. En este trabajo se ilustra la producción de un instrumento para la difusión de las indicaciones geográficas en el World Wide Web, utilizando únicamente software libre y freeware. Esta herramienta permite a todos los investigadores del Centro publicar su IG, la cual aparece como plenamente accesible a cualquier usuario final. Potencialmente, el hecho de permitir que este tipo de información sea plenamente accesible debería generar un gran impacto, acortando las distancias entre el trabajo realizado por los académicos y el usuario final. Creemos que es una óptima manera para que el público pueda acceder e interpretar la información espacial. En conclusión, esta plataforma debería servir para cerrar la brecha entre productores y usuarios de la información geográfica, permitiendo la interacción entre todas las partes así como la carga de nuevos datos dado un conjunto de normas destinadas a control de calidad

Forecasting and visualization of wildfires in a 3D geographical information system

[EN]This paper describes a wildfi re forecasting application based on a 3D virtual environment and a fi re simulation engine. A novel open source framework is presented for the development of 3D graphics applications over large geographic areas, off ering high performance 3D visualization and powerful interaction tools for the Geographic Information Systems (GIS) community. The application includes a remote module that allows simultaneous connection of several users for monitoring a real wildfi re event.

Toxics Release Inventory facilities and childhood cancer: Geographic information systems based approach

Purpose. To examine the association between living in proximity to Toxics Release Inventory (TRI) facilities and the incidence of childhood cancer in the State of Texas. ^ Design. This is a secondary data analysis utilizing the publicly available Toxics release inventory (TRI), maintained by the U.S. Environmental protection agency that lists the facilities that release any of the 650 TRI chemicals. Total childhood cancer cases and childhood cancer rate (age 0-14 years) by county, for the years 1995-2003 were used from the Texas cancer registry, available at the Texas department of State Health Services website. Setting: This study was limited to the children population of the State of Texas. ^ Method. Analysis was done using Stata version 9 and SPSS version 15.0. Satscan was used for geographical spatial clustering of childhood cancer cases based on county centroids using the Poisson clustering algorithm which adjusts for population density. Pictorial maps were created using MapInfo professional version 8.0. ^ Results. One hundred and twenty five counties had no TRI facilities in their region, while 129 facilities had at least one TRI facility. An increasing trend for number of facilities and total disposal was observed except for the highest category based on cancer rate quartiles. Linear regression analysis using log transformation for number of facilities and total disposal in predicting cancer rates was computed, however both these variables were not found to be significant predictors. Seven significant geographical spatial clusters of counties for high childhood cancer rates (p<0.05) were indicated. Binomial logistic regression by categorizing the cancer rate in to two groups (<=150 and >150) indicated an odds ratio of 1.58 (CI 1.127, 2.222) for the natural log of number of facilities. ^ Conclusion. We have used a unique methodology by combining GIS and spatial clustering techniques with existing statistical approaches in examining the association between living in proximity to TRI facilities and the incidence of childhood cancer in the State of Texas. Although a concrete association was not indicated, further studies are required examining specific TRI chemicals. Use of this information can enable the researchers and public to identify potential concerns, gain a better understanding of potential risks, and work with industry and government to reduce toxic chemical use, disposal or other releases and the risks associated with them. TRI data, in conjunction with other information, can be used as a starting point in evaluating exposures and risks. ^

Application of Text Summarization techniques to the Geographical Information Retrieval task

Automatic Text Summarization has been shown to be useful for Natural Language Processing tasks such as Question Answering or Text Classification and other related fields of computer science such as Information Retrieval. Since Geographical Information Retrieval can be considered as an extension of the Information Retrieval field, the generation of summaries could be integrated into these systems by acting as an intermediate stage, with the purpose of reducing the document length. In this manner, the access time for information searching will be improved, while at the same time relevant documents will be also retrieved. Therefore, in this paper we propose the generation of two types of summaries (generic and geographical) applying several compression rates in order to evaluate their effectiveness in the Geographical Information Retrieval task. The evaluation has been carried out using GeoCLEF as evaluation framework and following an Information Retrieval perspective without considering the geo-reranking phase commonly used in these systems. Although single-document summarization has not performed well in general, the slight improvements obtained for some types of the proposed summaries, particularly for those based on geographical information, made us believe that the integration of Text Summarization with Geographical Information Retrieval may be beneficial, and consequently, the experimental set-up developed in this research work serves as a basis for further investigations in this field.